Biophysics for Beginners: A Journey through the Cell Nucleus

528 Pages·2021·14.031 MB·English

by  Helmut Schiessel

Biophysics for
Beginners
Second Edition

Helmut Schiessel
Biophysics for
Beginners
A Journey through the Cell Nucleus
Second Edition
Publishedby
JennyStanfordPublishingPte.Ltd.
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BiophysicsforBeginners:AJourneythroughtheCellNucleus
(SecondEdition)
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Allrightsreserved.Thisbook,orpartsthereof,maynotbereproducedinany
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ISBN978-981-4877-80-0(Hardcover)
ISBN978-1-003-22310-8(eBook)
DOI:10.1201/9781003223108
Contents
PrefacetotheFirstEdition ix
PrefacetotheSecondEdition xii
1 MolecularBiologyoftheCell 1
1.1 TheCentralDogmaofMolecularBiology 1
1.2 AJourneythroughtheCellNucleus 8
2 StatisticalPhysics 19
2.1 ThePartitionFunction 19
2.2 Applications 33
2.3 TheEntropy 36
2.4 ParticleswithInteractionsandPhaseTransitions 45
2.5 BiomolecularCondensates 60
3 PolymerPhysics 79
3.1 RandomWalks 80
3.2 FreelyJointedandFreelyRotatingChains 84
3.3 TheRoleofSolventQuality 89
3.4 Self-AvoidingWalks 91
3.5 TheFloryArgument 94
3.6 TheBlobPicture 97
3.7 PolymersinPoorSolvents 101
3.8 InternalStructureofPolymers 106
4 DNA 113
4.1 TheDiscoveryoftheDNADoubleHelix 113
4.2 DNAontheBasePairLevel 118
4.2.1 AGeometricalApproach 118
4.2.2 AStatisticalPhysicsApproach 131
vi Contents
4.3 DNAasaWormlikeChain 146
4.4 DNAMelting 177
5 StochasticProcesses 191
5.1 Introduction 191
5.2 MarkovProcesses 196
5.3 MasterEquation 201
5.4 Fokker–PlanckEquation 203
5.5 Application:EscapeoveraBarrier 211
5.6 Application:DynamicForceSpectroscopy 215
5.7 LangevinEquation 221
5.8 Application:PolymerDynamics 225
6 RNAandProteinFolding 241
6.1 RNAFolding 241
6.2 ProteinFolding 247
7 ElectrostaticsinsidetheCell 265
7.1 Poisson–BoltzmannTheory 265
7.2 ElectrostaticsofChargedSurfaces 269
7.3 ElectrostaticsofCylindersandSpheres 278
7.4 Debye–Hu¨ckelTheory 284
7.5 BreakdownofMeanFieldTheory 292
8 DNA–ProteinComplexes 299
8.1 ProteinTargetSearch 299
8.2 RNAPolymerase 316
8.3 NucleosomeDynamics 327
8.3.1 SiteExposureMechanism 328
8.3.2 Force-InducedNucleosomeUnwrapping 337
8.3.3 NucleosomeSliding 356
8.4 ChromatinFibers 376
8.4.1 Two-AngleModel 378
8.4.2 Solenoid-TypeModels 388
8.5 ChromatinatLargeScales 397
8.5.1 FromClassicalPolymerstoFractalGlobules 399
8.5.2 FromPolymerRingstoLoopExtrusion 407
Contents vii
9 ComputationalMethods 421
9.1 MolecularDynamicsSimulations 422
9.2 MonteCarloSimulations 425
AppendixA: ProbabilityTheory 445
AppendixB: TheDistributionofMagnetizationandthe
CentralLimitTheorem 451
AppendixC: ConnectionbetweenPolymerStatisticsand
CriticalPhenomena 453
AppendixD: Hamilton’sPrincipleandthePendulum 465
AppendixE: FourierSeries 473
AppendixF: ThePre-AveragingApproximation 477
AppendixG: InteractionbetweenTwoEquallyCharged
PlatesatZeroTemperature 483
AppendixH: GeometriesofChromatinFiberModels 487
References 491
Index 503

Preface to the First Edition
Preface to the first edition: Biophysics or biological physics or
statistical physics of biological matter or quantitative biology or
computational biology is a large and rapidly growing interdisci-
plinary field with many names on the border between physics,
biology and mathematics. It is not clear where this field begins,
where it ends, or where it will ultimately lead. However, it is
clear that tremendous progress has been made in this area over
the past two decades. This book is the result of various attempts
to teach the subject in a variety of settings to audiences from
diverse backgrounds at different stages in their studies. It started
with courses (usually 4 h long) at winter and summer schools
in Denmark, the Netherlands, Belgium, South Korea, South Africa,
France and Mexico. The material was expanded in a theoretical
biophysicscourseforPhysicsMastersstudentsatLeidenUniversity.
A script that I made for a course at the Casimir Graduate School
betweenDelftandLeidenUniversitywasashortfirstversionofthe
book.
WhenIdecidedtowriteanentirebookonthesubject,Iwanted
it to be self-contained (avoiding phrases like “one can show”),
especially since I noticed that some students in my classes did
not know much about molecular biology while others had no
background in statistical physics. In order for the book to reach a
certain depth without becoming too thick, some difficult decisions
had to be made beforehand. I decided that everything in this
book should be related to what I consider the heart of molecular
biology of the cell, the central dogma of molecular biology, which
states that information flows from DNA to RNA to proteins. By
limiting myself to this topic, I only had to deal with three types
of molecules, all polymers, all of which are in the nucleus of